Preheat the oven to 350 degrees F. Grease a 9x13 pan with nonstick cooking spray and set aside.
In a medium skillet, melt the butter over medium heat. Once melted, turn up the heat to medium high. Continue stirring and look for small golden bits that will start to settle on the bottom of the pan. This should take around 3 to 5 minutes and the butter will have a nutty aroma. Once this happens, take it off the heat and pour into a medium, heat-safe bowl to cool while you prepare the other ingredients.
In a medium bowl, whisk together the flour, baking soda, salt, cinnamon, ginger, nutmeg, and cloves. Set aside.
In a large bowl, combine the brown butter, brown sugar, and granulated sugar. Mix with a spoon or spatula until smooth. Add in the egg, egg yolk, pumpkin, and vanilla and stir until well combined.
Add the dry ingredients and stir until just combined, don't over mix. Stir in the chocolate chunks.
Pour the batter evenly into the prepared pan. Sprinkle with sea salt flakes, if using. Bake the bars for 28 to 35 minutes or until the bars are set and golden brown around the edges.
Let the bars cool completely before cutting into squares.